What do I do with a package that is delivered to lab?: Open, figure out if it is VDS, show to Owais or John G. if there, Label appropriately, Place in proper storage, Place receipt in Dr. B's pigeon hole by the lab notebooks and let him know it has arrived and is stored properly.
NOTES FOR THIS WEEK'S LAB:
Precision & Accuracy - the error bars don't show up that well. So, have them add a row that is Standard Deviation x 3 (or x5 or x10). Then use that for their error bars.
TA Tasks
Pre-Lab Q's, Post Lab Q's
Committee Meeting questions and discussion topics
Go over Lab Notebook Grading Rubric & Lab Notebook spreadsheet
Revise Lab Notebook Grading Rubric (?) - DONE Dr. B
Lab Notebook penultimate grading after Mentors have provided comments and rough score.
Make Sign-In Sheet for Lab (for PAI 2.14 folder) - will probably be 2 sheets each week (in Gdocs, download, edit and re-upload). Must match the order on Canvas. So, cross check as we have ADD/DROPS.
Modify LabNotebook Reviewing assignments sheet in VDSStaff GDocs.
-- assign each mentor to the students in their group - DONE
Make "Assignments" for Lab Notebooks in Canvas (e.g. LabNoteA, LabNoteB, etc.)
- these need to be there so that students can see the Due Dates along with other 'electronic'
assignments.
- for now, just put due date for LabNoteA. Create the others, but leave them without a due date.
Start creating the Assignment names in Canvas (e.g. Labnotebook A, B, C and Beer's Law Report)
- assign each a point value of '10'
- make it either a 'paper' submission or restrict to a 'PDF' for electronically submitted work
Lead Lab Safety - DONE
- Melissa works with 2 mentors to
- implement training (in lab and online and videos with quizzes)
- verification that training (in lab and online) is completed
- create a 'Lab Safety Training Sheet turned in to binder' assignment on Canvas with a due date of Monday night of next week.
Teach a Module In Class
- Melissa: Beer's law. (on Feb. 3rd or Feb 9th) Download old SP14 slides from last year's Canvas course to prep
- Oscar: Mini-Research presentation (before summer fellowship applications are due) with activity on evaluating a piece of data (graph, pymol image, etc)
MENTOR TASKS
NOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. However, some tasks say 'All' so your name won't show up specificallly - Thanks, Dr. B
----- this assumes I haven't misspelled your name!
'Starter Questions' for the TEAM meetings - to help your students get to know you better
QUESTIONS FOR THE WHOLE GROUP
Favorite place on the Drag (or around the 40 acres but not on campus)?
Where are you from? What high school did you go to?
How is your adjustment to UT going?
Favorite/Least favorite classes this semester? Any particular classes you are concerned about?
What are your majors?
What are your career interests?
What do you think of VDS so far? Favorite aspects? Least favorite aspects?
Which do you prefer - wet lab or computer labs?
Do you have any concerns about the labs?
Do you have any questions regarding the concepts underlying the labs?
What do you hope to get out of this experience?
What are your research interests?
Since this is VDS, what is your favorite drug/molecule?
General points to cover (by the TEAM leaders):
- basic intro (major, year, etc.)
- overview of what they can expect from VDS (short- and long-term)
- how VDS has helped you and why it is beneficial for them to stick with it
- your research interests and experiences
- your career plans and what stage you are at now
- Why VDS is the best stream!
RUBRICS
post Labnotebook Grading rubric to Wiki (upload PDF to GDocs for VDSclass/Misc account - not VDSStaff, then in space.menu on lhs - make link to file, verify link works) - Alberto
post Labnotebook vs LabReport to Wiki (upload PDF to GDocs for VDSclass/Misc account - not VDSStaff, then in space.menu on lhs - make link to file, verify link works) - Andee
Use the MentorLabLog on GDocs/VDSstaff for a Lab Notebook for Wet Lab tasks - ALL
Lab Safety (Saturday, Sunday, Monday)
LAB SAFETY MENTORS: Andee, Charina
LAB SAFETY TA: Melissa
Update Lab Safety page in Wikispaces with names of each students and table, link from left hand menu.
See Lab Safety Folder in GDrive/VDSstaff
- Practice & Plan Lab Safety Walk Throughs.
- Lab Safety Videos posted to Wikispaces and to Canvas
-- they will watch these and complete a quiz before doing Lab 2 Buffer & Solutions (ok for them to do Lab 1 without)
- Generate Quizzes in Canvas - see GDrive/VDSStaff/.
-- use the questions in the Prelab 2-Safety Videos.docx to make the quiz in canvas.
See GDrive/VDSStaff/Spring15LabsforTesting to see the revised procotols
LAB WORK
Make small scale YopH and FtHap the same way that the students will - ALL (except John and Avery)
-- Transformation, Expression, Sonication
-- Purification (Ni-NTA), FPLC, Storage in 20% Glycerol in -20degC.
--- QUESTIONS:
Do we get enough to do enzyme assays?
Is it stable for a month in storage being so dilute
Enzyme Assay with Phosphatase - ALL (except Andy and Cidia)
- use YopH or FtHap that you made
Beer’s Law lab (it has been changed from last year) - ALL
Virtual Screening labs to check for errors/unclear items in the protocol. Report them to Dr. B (just comment on the protocol and email Dr. B)
Revised VS1 lab - John, Alberto
TO BE DONE WITHIN 2 WEEKS:
Transformation & Midi Prep of plasmids in DH5alpha
YopH pNIC-Bsa4 in DH5alpha – for Midiprep - Brianna
FtHap pNIC-Bsa4 in DH5alpha - for Midiprep - Cidia
Blue Juice for protein gels - (need DTT - check first) - Brianna (can be done later)
Titration lab Demonstration - Charina
Virtual Screening labs to check for errors/unclear items in the protocol. Report them to Dr. B (just comment on the protocol and email Dr. B)
Revised VS Phosphatase (replaces VS2 and VS3) - Nikki, Cidia, John, Brianna,
Rinse the 'clean' collirollers in nanopure water, transfer to a clean bottle, label - then Autoclave (use autoclave tape) - Alberto (have Melissa train you on autoclave)
Divide up colirrolers in to 6 rollers each in sterile tubes of (600 ul tubes) - make a full ~ 80 tube rack of these - Alberto
Autoclave Nanopure water, label, store in Cubby. Make 2 x 500ml. - this is for 1st Lab to make 30% EtOH - Alberto
-
Teaching Points for Labs Sp15 (insert Link)
-- also see folder in VDS Staff Google Docs account -- contains lab handout and teaching points sheets
EXAMPLE TEACHING POINTS NOTES for PyMol 1
- show them Alt + i + t for time stamp
- have them open and use UTBox
- how to force Firefox to download a file to a folder you specify
- don't need pics for Warmups
- their Word doc does not need to be typed verbatim from handout. They can copy and paste the procedure steps, but must add in comentary/analysis
Comment on Lab Notebooks (see your assignments on the **LabNotebookCommentingforMentorsSp14** in VDSStaff GDocs) (UPDATE LINK) - ALL
-- After the students turn their lab notebooks in on Fridays and Saturdays, you can begin commenting.
---------(they turn them in on Saturday at the latest - but once a grading rubric is on there - you can start looking at it.)
-- for the 4-5 notebooks which you have been assigned, go through them and write comments directly in the notebook (blu ink preferred)
-- Also, as you go, please circle or underline items on the Lab Notebook Grading Rubric that would help TAs in grading. (e.g. missing analysis, materials not listed, no page numbers, etc.)
-- Joey will go back through and apply a score to each one. Then Dr. B will approve them. DUE DATE: Monday night/Tuesday during the day of PyMol1 week - so that Joey and I have time to look at them.
WIKISPACES WORK
create Wikispaces pages for each student for Protein Labs (create new page Protein Labs Sp15) - Alberto
CATALOGING PURCHASING INTO EXCEL SPREADSHEET FROM FALL 14
-- place receipts in Dr. B's receipts pigeon hole - John
Express, Purify, FPLC, Characterize and store in 20% glycerol YopH
Make 2L of LB
OLD LAB TECH STUFF
transform YopH and FtHap again - DONE
grow up colonies of each, mini prep, send to DNA sequencing
make 5L of LB media and autoclave
make 45 LB plates without any antibiotics - for Fun Plates - DONE
IPTG - 0.1 M IPTG (200 ul each) x 45
Kanamycin - 50mg/ml stocks (about 100 ul each) x 45 - DONE
Print Protocols that you need for the week Make more LB+ Kanamycin plates Make more LB
Transform both Fthap and YopH into BL21(DE3) cells on Kanamycin plates - do one transformation for each - but split into th 2 plates (a Hi density and a Low density). Will have 4 plates total
Grow up a colony from each of the OLD YopH and FtHap plates to determine if they are any good
- put 5ml of LB + 5 ul of Kanamycin in a 14 ml round bottom, snap-cap transformation tube
- grow at 37degC overnight in shaker (dry or water bath shaker)
- keep track of which culture came from which plate
- if a culture does not grow by the morning- we can throw out the plate
Make IPTG - see recipe below
Make Lysozyme - see recipe below
TUESDAY - start expressions (use Expression protocol from Fall 2013 (v. 5) in GDrive) For YopH Only (just concentrate on this protein for now. You will do FtHap later) Express Note: Luis, Oscar, Melissa and Avery will be helping you out with this (Dr. B is too lazy!)
In morning (9 or 9:30 am) start several small cultures (5ml) + Kan
- let grow for 8 hrs
Then move on to - overnight IPTG induction method of at least 2 liters
Also, concurrently start - small cultures overnight for next day 4 hr IPTG induction method of at least 2 liters
ORDER
- 0.45 micron sringe filters - see board for Cat #
- 10ml syringes - see board
- NaCl - Biosci
- NaOH - Biosci
Purify - via Nickel column Characterize FPLC with G75 column (need to make sure this one is on there beforehand) Storage
FtHAP and YopH
Express, Purify, Characterize, and Store in same way that the Springers will do it (i.e. small scale - 25-50 ml))
- will include IPTG induction this year!
Run through Beer's Law using pNP instead of Blue/Red dye
VDS Class Assistant Tasks- Eric B
Mini-Research Write Up - Done
see last year's page: http://vdsstream.wikispaces.com/Mini+Research+Write+Ups+Sp14
Delete old pages
make new version of the wiki page from Sp14 page for Sp15
- put link to it on left hand side menu of our Wiki
make a copy of the form for Sp15. It is in GDrive/VDSstaff/MiniResearchWiki/MiniResearchWikiSp14
- NAMED: Mini Research Write Up Disease Selection Sp14 [Form]
clear the existing data in form and link to Wikipage.
email out to students Via Canvas
- monitor daily for disease requests, accept or reject
After they have turned in their 1st Mini Research Write Up as PDF
Create a Wikispaces page for each Disease of the Mini-Research Write Ups (no student names on there)
Create 20 Questions form to send out to students (once)
make 2 versions of the form so that all 42 of the MiniResearch pages have a question about them
Each form can be 21 questions. It could be a
- use old Sp 14 form
Create MiniReserach Wiki Voting form - see old one and revise
Lit Search and Bibliography assignment reviewing (see ReviewingLitSearchforMentorsGDocsSp14 in VDSStaff GDocs) (UPDATE LINK)- Done
-- determine # of days late for each student using the Image file in the same folder that has the submission dates -- submissions are in Canvas, print them out, write directly on the papers and indicate points off out of total points and then indicate # of points off for days late. DUE DATE: Monday 16th during the day - so that Dr. B can hand them back in class on Tuesday
WIKILOGINS
check that everyday and approve them being added to the wikispaces IF
1. they have a recognizable username that starts with their FirstnameLastInitial
e.g. WilliamB (or at least something pretty close so that we can tell who they are)
- if they don't - email them to change it
2. they are actually on the roster (so we don't have any rogue wiki editors....)
Wikispaces may send a message via email when people submit to join - otherwise you will just need to check it.
Oscar & Melissa and I will also check it closer to their due date (Sunday).
NOTEBOOK REVIEWING SHEET for LabNotebook B (Beer's and PyMol1)- SKIP THIS (Oscar had already made it) - Done LabBook C
Also, would you mind updating the sheet in GDrive /VDSSTAFF "LabNotebookCommentingforMentorsSpring15forMentors" and basically roll each mentor down by one. And alternate the TAs (e.g. Oscar gets who Melissa had and Melissa gets who Oscar had).
Let's change the numbers for some
Avery 6
Nikki 5
Charina 5
Andrea 5
John G 4
Cidia 5
Brianna 6
Alberto 5
Total: 41
(we had one student Q drop - (so, she can be removed from everything - rosters, gade sheets, etc)
We need to update the pairings - but keep at least one someplace (another sheet or on the same sheet) where we have the old pairings for the 1st Lab Notebook (call it LabNotebokA)
The new one can be LabNotebookB
PRE-Qs- Done Grade Pre-Q's for PyMol2
- see Canvas
- mute assignment first, then grade them
Create Peer Review assignments for Beer's Law Lab Report (i.e. who gets which report - let Dr. B see in case we need to adjust some for better matchups)- Done
- this can't be done until the submit their original Beer's Law Lab reports (i.e. after Sunday Feb 22nd)
Schedule 2nd round of TA meetings with each individual student -1st one done by Avery and Oscar - Done
- these will be the Week of PyMol3
Enter finalized Lab Notebook grades to Canvas (maybe every 2 week or every 3 weeks as determined by the schedule) - Done
print 40 photorelease forms
WEEKLY TASKS
COMPLETED THINGS:
-- Upload 2014 Posters to the VDS Google Website (poster are in GDrive/posters for the VDSclass Google account)
- update purchasing spreadsheet using receipts in the Pigeon Hole marked 'VDS Receipts'
SOLUTIONS RECIPES & INSTRUCTIONS:
(also see the Solutions&Dilutions Spreadsheet on GDocs for help with calculations)
Make LB - 2Liters - and autoclave Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)
(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
Printer Installation
Login as Mentor, Start Menu,
Devices And printers
Add New Printer
Add "local" printer
Create New Port --> standard TCP pathway
Enter IP 128.82.195.186
Printer Name Lexmark C543
Add Printer (if can't find printer do Window Update)
For installation of a different Printer (such as Dell) change the IP address and Printer Name
Make a COPY of the Fall 14 Schedule for mentors - Dr. B - Done
Re-name for Spring2015 - Dr. B - DONE
Update with new Mentor names - Dr. B - DONE
Link to appropriate places/pages (e.g. Wikispaces nagivation bar on left - Dr. B may have to do this though) - Melissa
come up with a lab 'mission statement' - ALL
Please Print, Read and Sign the Mentor Contracts. Then return to Dr. B - ALL --- Mentor Contract on GDocs
update your mentor schedules - ALL (once Gdrive sheet is made)
update Class Schedule -
Make a VDS Staff Picture Page - Nikki
- see previous /Mentor Pics' page (MentorPicsSp14)
- take pics of all Staff
- create new Wikipage, link to the navigation menu on the left, post each pic and add labels
Take pictures of staff (group and individuals - upload to VDSStaff in GDocs, Upload to Wiki Mentors Sp15 page) -
Generate a time sheet - PAID MENTORS
LAB CLEANING - ALL
clean out top loading -20degC freezer - make sure all boxes are labelled get rid of old plates, solutions, sample tubes, and concentrator tubes in -20degC -
organize and label -80degC freezer racks -
unpacking supplies, labeling and storing them
SCHEDULING
Create new class schedule sheet for WHOLE class in Google Drive spreadsheet - Avery (DONE)
- this is where they put down their own class schedules
- update link on front page of Canvas for VDS class site -
- push the sheet out to students with instructions (wait til Canvas has all the students)
Create a Sign Up spreadsheet for the 1st week of class/lab - Avery (DONE)
- sign ups for Lab Safety Walk Throughs (coordinate with Safety Mentors and Melissa - when these will be) - I need to know these times by Monday.
- sign ups for Precision & Accuracy lab (pipetting exercise)
- use previous versions of sign up sheet from Spring 14 as a template (put it in the GDrive/VDSclass/Scheduling folder)
- create new Wikispaces page that shows the spreadsheet embedded and has links that allow students to go to the sheet and edit and enter the time they want
- push the sheet out to students with instructions (wait til Canvas has all the students)
By Saturday of 1st week - assign each student to a Team with a mentor (or two mentors) - Avery (DONE)
- maybe create a TEAMS page on Wikispaces or on Canvas for everyone to see their assignments.
- team meetings will start at the end of the 2nd Week
In 'Pigeon Holes' for lab notebooks (Sunday or Monday)
organize pigeon holes by moving VDS Alums to the other lab notebook stacks - Cidia, Nikki
make new name plate sheets (out of manila folders) - Cidia, Nikki
Organize binders (Student one and Mentor one) -
Mentor Folder:
create and print new hourly sign-in sheet (don't need to do TA though) - see old one in GDocs either VDSStaff or /Mentors - Andee
Student Folder:
remove old safety training (except for people still working in lab (e.g. mentors and researchers) - Andee
put new sign in sheet for students (get from the TA) - TBD LATER - don't have roster yet
make picture roster of students and staff pics (get photo roster from Dr. B - but add in staff pictures) - TBD LATER - don't have roster yet
Mentor name tags with VDS logo on them (talk to Dr. B - may have to use Dr. B's printer? Might work on lab printer in manual feed mode) - Brianna
- see hold name tags file in GDrive VDSclass login /Misc/NameBadgeLabels
-- create new folder /MentorsSpring15
Lab Beer's Law - Brianna, Alberto
Lab Precision & Accuracy - Nikki, John G., (do Sunday preferably)
First pipetting steps with Excel graph
Lab Buffers & Solutions (modified solution)
200 ml 0.1 M Tris Base pH 7.5 – pH meter, acids (calibrate pH meter as part of this, test out new pH probes)- Cidia
Kanamycin – syringe filter -Avery
Calculate lowest concentration of a stock enzyme that is acceptable for enzyme assay lab (draft protocol in GDrive/VDSStaff/Spring15Labs) - Cidia
SMALL CULTURES
Put small cultures (8hrs ones) into fridge for expression tomorrow - ALL (except John and Avery)
- Melissa made several in the AM for you to use
TABLE OF CONTENTS:
TA Tasks
- TAs: Oscar, MelissaMENTOR TASKS
- Mentors: Alberto T.C., Andee F., Avery W., Charina B., Cidia G., John G., Nikki W., Brianna G.- Research Guru: Luis V.
Lab Tech/Mentor Tasks ++++++++++++
- John G.VDS Class Assistant Tasks
- Eric B.SOLUTIONS Recipes & Instructions
What do I do with a package that is delivered to lab?:
Open, figure out if it is VDS, show to Owais or John G. if there, Label appropriately, Place in proper storage, Place receipt in Dr. B's pigeon hole by the lab notebooks and let him know it has arrived and is stored properly.
NOTES FOR THIS WEEK'S LAB:
Precision & Accuracy
- the error bars don't show up that well. So, have them add a row that is Standard Deviation x 3 (or x5 or x10). Then use that for their error bars.
TA Tasks
Pre-Lab Q's, Post Lab Q'sCommittee Meeting questions and discussion topics
Go over Lab Notebook Grading Rubric & Lab Notebook spreadsheet
Revise Lab Notebook Grading Rubric (?) - DONE Dr. B
Lab Notebook penultimate grading after Mentors have provided comments and rough score.
Make Sign-In Sheet for Lab (for PAI 2.14 folder) - will probably be 2 sheets each week (in Gdocs, download, edit and re-upload). Must match the order on Canvas. So, cross check as we have ADD/DROPS.
Modify LabNotebook Reviewing assignments sheet in VDSStaff GDocs.
-- assign each mentor to the students in their group - DONE
Make "Assignments" for Lab Notebooks in Canvas (e.g. LabNoteA, LabNoteB, etc.)
- these need to be there so that students can see the Due Dates along with other 'electronic'
assignments.
- for now, just put due date for LabNoteA. Create the others, but leave them without a due date.
Start creating the Assignment names in Canvas (e.g. Labnotebook A, B, C and Beer's Law Report)
- assign each a point value of '10'
- make it either a 'paper' submission or restrict to a 'PDF' for electronically submitted work
Lead Lab Safety - DONE
- Melissa works with 2 mentors to
- implement training (in lab and online and videos with quizzes)
- verification that training (in lab and online) is completed
- create a 'Lab Safety Training Sheet turned in to binder' assignment on Canvas with a due date of Monday night of next week.
Teach a Module In Class
- Melissa: Beer's law. (on Feb. 3rd or Feb 9th) Download old SP14 slides from last year's Canvas course to prep
- Oscar: Mini-Research presentation (before summer fellowship applications are due) with activity on evaluating a piece of data (graph, pymol image, etc)
MENTOR TASKS
NOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. However, some tasks say 'All' so your name won't show up specificallly - Thanks, Dr. B----- this assumes I haven't misspelled your name!
Lab Safety mentors - Charina, Andee
Buffer Titration mentor - Charina
Scheduling mentor - Avery
MiniRes mentors (assignment and voting) -
Outreach mentor -
Peer Review Mentor -
Please fill out your weekly schedule here:- ALLhttps://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodElfeldhQlFDeUZJa3pqdkMtQ1VkdUE&usp=sharing
linkupdated 01/18/2015 at 2:24 pm
'Starter Questions' for the TEAM meetings - to help your students get to know you better
QUESTIONS FOR THE WHOLE GROUP
General points to cover (by the TEAM leaders):
- basic intro (major, year, etc.)- overview of what they can expect from VDS (short- and long-term)
- how VDS has helped you and why it is beneficial for them to stick with it
- your research interests and experiences
- your career plans and what stage you are at now
- Why VDS is the best stream!
RUBRICS
post Labnotebook Grading rubric to Wiki (upload PDF to GDocs for VDSclass/Misc account - not VDSStaff, then in space.menu on lhs - make link to file, verify link works) - Alberto
post Labnotebook vs LabReport to Wiki (upload PDF to GDocs for VDSclass/Misc account - not VDSStaff, then in space.menu on lhs - make link to file, verify link works) - Andee
Use the MentorLabLog on GDocs/VDSstaff for a Lab Notebook for Wet Lab tasks - ALL
Lab Safety (Saturday, Sunday, Monday)
LAB SAFETY MENTORS: Andee, CharinaLAB SAFETY TA: Melissa
Update Lab Safety page in Wikispaces with names of each students and table, link from left hand menu.
See Lab Safety Folder in GDrive/VDSstaff
- Practice & Plan Lab Safety Walk Throughs.
- Lab Safety Videos posted to Wikispaces and to Canvas
-- they will watch these and complete a quiz before doing Lab 2 Buffer & Solutions (ok for them to do Lab 1 without)
- Generate Quizzes in Canvas - see GDrive/VDSStaff/.
-- use the questions in the Prelab 2-Safety Videos.docx to make the quiz in canvas.
See GDrive/VDSStaff/Spring15LabsforTesting to see the revised procotols
LAB WORK
Make small scale YopH and FtHap the same way that the students will - ALL (except John and Avery)
-- Transformation, Expression, Sonication
-- Purification (Ni-NTA), FPLC, Storage in 20% Glycerol in -20degC.
--- QUESTIONS:
Enzyme Assay with Phosphatase - ALL (except Andy and Cidia)
- use YopH or FtHap that you made
Beer’s Law lab (it has been changed from last year) - ALL
Virtual Screening labs to check for errors/unclear items in the protocol. Report them to Dr. B (just comment on the protocol and email Dr. B)
TO BE DONE WITHIN 2 WEEKS:
Transformation & Midi Prep of plasmids in DH5alpha
Blue Juice for protein gels - (need DTT - check first) - Brianna (can be done later)
Titration lab Demonstration - Charina
Virtual Screening labs to check for errors/unclear items in the protocol. Report them to Dr. B (just comment on the protocol and email Dr. B)
Rinse the 'clean' collirollers in nanopure water, transfer to a clean bottle, label - then Autoclave (use autoclave tape) - Alberto (have Melissa train you on autoclave)
Divide up colirrolers in to 6 rollers each in sterile tubes of (600 ul tubes) - make a full ~ 80 tube rack of these - Alberto
Autoclave Nanopure water, label, store in Cubby. Make 2 x 500ml. - this is for 1st Lab to make 30% EtOH - Alberto
-
Teaching Points for Labs Sp15 (insert Link)
-- also see folder in VDS Staff Google Docs account
-- contains lab handout and teaching points sheets
EXAMPLE TEACHING POINTS NOTES for PyMol 1
- show them Alt + i + t for time stamp
- have them open and use UTBox
- how to force Firefox to download a file to a folder you specify
- don't need pics for Warmups
- their Word doc does not need to be typed verbatim from handout. They can copy and paste the procedure steps, but must add in comentary/analysis
Comment on Lab Notebooks (see your assignments on the **LabNotebookCommentingforMentorsSp14** in VDSStaff GDocs) (UPDATE LINK) - ALL
-- After the students turn their lab notebooks in on Fridays and Saturdays, you can begin commenting.
---------(they turn them in on Saturday at the latest - but once a grading rubric is on there - you can start looking at it.)
-- for the 4-5 notebooks which you have been assigned, go through them and write comments directly in the notebook (blu ink preferred)
-- Also, as you go, please circle or underline items on the Lab Notebook Grading Rubric that would help TAs in grading. (e.g. missing analysis, materials not listed, no page numbers, etc.)
-- Joey will go back through and apply a score to each one. Then Dr. B will approve them.
DUE DATE: Monday night/Tuesday during the day of PyMol1 week - so that Joey and I have time to look at them.
WIKISPACES WORK
CATALOGING PURCHASING INTO EXCEL SPREADSHEET FROM FALL 14
-- place receipts in Dr. B's receipts pigeon hole - John
++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++
LAB TECH/MENTOR TASKS - John G +++++++++++++++++++++++++
RECENT LAB TECH STUFF
DNA sequences
- use Sequence Manipulation suite (website) to translate all 3 reading frames
- BLASTP these against the protein sequences to see if any of the 3 match YopH
-- Do NOT blast againt the nucelotide sequence
Old WIkispaces page for YopH (may not be accurate)
http://vdsstream.wikispaces.com/Target+-+Protein-Tyrosine+Phosphatase+Yersinia+pestis+YopH+%28Bubonic+Plague%29
YopH protein:
1 MRERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACG
61 GEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVL
121 AVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQK
181 TISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIH
241 CRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQG
301 RPLLNSX
Express, Purify, FPLC, Characterize and store in 20% glycerol YopH
Make 2L of LB
OLD LAB TECH STUFF
transform YopH and FtHap again - DONE
grow up colonies of each, mini prep, send to DNA sequencing
make 5L of LB media and autoclave
make 45 LB plates without any antibiotics - for Fun Plates - DONE
IPTG - 0.1 M IPTG (200 ul each) x 45
Kanamycin - 50mg/ml stocks (about 100 ul each) x 45 - DONE
Print Protocols that you need for the week
Make more LB+ Kanamycin plates
Make more LB
Transform both Fthap and YopH into BL21(DE3) cells on Kanamycin plates
- do one transformation for each - but split into th 2 plates (a Hi density and a Low density). Will have 4 plates total
Grow up a colony from each of the OLD YopH and FtHap plates to determine if they are any good
- put 5ml of LB + 5 ul of Kanamycin in a 14 ml round bottom, snap-cap transformation tube
- grow at 37degC overnight in shaker (dry or water bath shaker)
- keep track of which culture came from which plate
- if a culture does not grow by the morning- we can throw out the plate
Make IPTG - see recipe below
Make Lysozyme - see recipe below
TUESDAY - start expressions (use Expression protocol from Fall 2013 (v. 5) in GDrive)
For YopH Only (just concentrate on this protein for now. You will do FtHap later)
Express
Note: Luis, Oscar, Melissa and Avery will be helping you out with this (Dr. B is too lazy!)
In morning (9 or 9:30 am) start several small cultures (5ml) + Kan
- let grow for 8 hrs
Then move on to
- overnight IPTG induction method of at least 2 liters
Also, concurrently start
- small cultures overnight for next day 4 hr IPTG induction method of at least 2 liters
ORDER
- 0.45 micron sringe filters - see board for Cat #
- 10ml syringes - see board
- NaCl - Biosci
- NaOH - Biosci
Purify - via Nickel column
Characterize
FPLC with G75 column (need to make sure this one is on there beforehand)
Storage
FtHAP and YopH
Express, Purify, Characterize, and Store in same way that the Springers will do it (i.e. small scale - 25-50 ml))
- will include IPTG induction this year!
Run through Beer's Law using pNP instead of Blue/Red dye
VDS Class Assistant Tasks- Eric B
Mini-Research Write Up - Done
see last year's page:
http://vdsstream.wikispaces.com/Mini+Research+Write+Ups+Sp14
Delete old pages
make new version of the wiki page from Sp14 page for Sp15
- put link to it on left hand side menu of our Wiki
make a copy of the form for Sp15. It is in GDrive/VDSstaff/MiniResearchWiki/MiniResearchWikiSp14
- NAMED: Mini Research Write Up Disease Selection Sp14 [Form]
clear the existing data in form and link to Wikipage.
email out to students Via Canvas
- monitor daily for disease requests, accept or reject
After they have turned in their 1st Mini Research Write Up as PDF
- Create a Wikispaces page for each Disease of the Mini-Research Write Ups (no student names on there)
- Create 20 Questions form to send out to students (once)
- make 2 versions of the form so that all 42 of the MiniResearch pages have a question about them
- Each form can be 21 questions. It could be a
- use old Sp 14 formLit Search and Bibliography assignment reviewing (see ReviewingLitSearchforMentorsGDocsSp14 in VDSStaff GDocs) (UPDATE LINK)- Done
-- determine # of days late for each student using the Image file in the same folder that has the submission dates
-- submissions are in Canvas, print them out, write directly on the papers and indicate points off out of total points and then indicate # of points off for days late.
DUE DATE: Monday 16th during the day - so that Dr. B can hand them back in class on Tuesday
WIKILOGINS
check that everyday and approve them being added to the wikispaces IF
1. they have a recognizable username that starts with their FirstnameLastInitial
e.g. WilliamB (or at least something pretty close so that we can tell who they are)
- if they don't - email them to change it
2. they are actually on the roster (so we don't have any rogue wiki editors....)
Wikispaces may send a message via email when people submit to join - otherwise you will just need to check it.
Oscar & Melissa and I will also check it closer to their due date (Sunday).
NOTEBOOK REVIEWING SHEET for LabNotebook B (Beer's and PyMol1)- SKIP THIS (Oscar had already made it) - Done LabBook C
Also, would you mind updating the sheet in GDrive /VDSSTAFF "LabNotebookCommentingforMentorsSpring15forMentors" and basically roll each mentor down by one. And alternate the TAs (e.g. Oscar gets who Melissa had and Melissa gets who Oscar had).
Let's change the numbers for some
Avery 6
Nikki 5
Charina 5
Andrea 5
John G 4
Cidia 5
Brianna 6
Alberto 5
Total: 41
(we had one student Q drop - (so, she can be removed from everything - rosters, gade sheets, etc)
We need to update the pairings - but keep at least one someplace (another sheet or on the same sheet) where we have the old pairings for the 1st Lab Notebook (call it LabNotebokA)
The new one can be LabNotebookB
PRE-Qs- Done
Grade Pre-Q's for PyMol2
- see Canvas
- mute assignment first, then grade them
Create Peer Review assignments for Beer's Law Lab Report (i.e. who gets which report - let Dr. B see in case we need to adjust some for better matchups)- Done
- this can't be done until the submit their original Beer's Law Lab reports (i.e. after Sunday Feb 22nd)
Schedule 2nd round of TA meetings with each individual student -1st one done by Avery and Oscar - Done
- these will be the Week of PyMol3
Enter finalized Lab Notebook grades to Canvas (maybe every 2 week or every 3 weeks as determined by the schedule) - Done
print 40 photorelease forms
WEEKLY TASKS
COMPLETED THINGS:
-- Upload 2014 Posters to the VDS Google Website (poster are in GDrive/posters for the VDSclass Google account)
- update purchasing spreadsheet using receipts in the Pigeon Hole marked 'VDS Receipts'
SOLUTIONS RECIPES & INSTRUCTIONS:
(also see the Solutions&Dilutions Spreadsheet on GDocs for help with calculations)Make LB - 2Liters - and autoclave
Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
Printer Installation
- Login as Mentor, Start Menu,
- Devices And printers
- Add New Printer
- Add "local" printer
- Create New Port --> standard TCP pathway
- Enter IP 128.82.195.186
- Printer Name Lexmark C543
- Add Printer (if can't find printer do Window Update)
For installation of a different Printer (such as Dell) change the IP address and Printer NamePrinter Name: Lexmark C543 IP: 128.83.195.186
Printer Name: Dell IP: 129.116.152.49
COMPLETED STUFF++++++++++++++++++++++++++++++++++++++++++++++++++++++++
MENTOR TASKS FOR 1st MENTOR MEETING
Make a COPY of the Fall 14 Schedule for mentors - Dr. B - Done
Re-name for Spring2015 - Dr. B - DONE
Update with new Mentor names - Dr. B - DONE
Link to appropriate places/pages (e.g. Wikispaces nagivation bar on left - Dr. B may have to do this though) - Melissa
Calendar for Staff Sp15
come up with a lab 'mission statement' - ALLPlease Print, Read and Sign the Mentor Contracts. Then return to Dr. B - ALL
--- Mentor Contract on GDocs
update your mentor schedules - ALL (once Gdrive sheet is made)
update Class Schedule -
Make a VDS Staff Picture Page - Nikki
- see previous /Mentor Pics' page (MentorPicsSp14)
- take pics of all Staff
- create new Wikipage, link to the navigation menu on the left, post each pic and add labels
Take pictures of staff (group and individuals - upload to VDSStaff in GDocs, Upload to Wiki Mentors Sp15 page) -
Generate a time sheet - PAID MENTORS
LAB CLEANING - ALL
clean out top loading -20degC freezer - make sure all boxes are labelled
get rid of old plates, solutions, sample tubes, and concentrator tubes in -20degC -
organize and label -80degC freezer racks -
unpacking supplies, labeling and storing them
SCHEDULING
Create new class schedule sheet for WHOLE class in Google Drive spreadsheet - Avery (DONE)
- this is where they put down their own class schedules
- update link on front page of Canvas for VDS class site -
- push the sheet out to students with instructions (wait til Canvas has all the students)
Create a Sign Up spreadsheet for the 1st week of class/lab - Avery (DONE)
- sign ups for Lab Safety Walk Throughs (coordinate with Safety Mentors and Melissa - when these will be) - I need to know these times by Monday.
- sign ups for Precision & Accuracy lab (pipetting exercise)
- use previous versions of sign up sheet from Spring 14 as a template (put it in the GDrive/VDSclass/Scheduling folder)
- create new Wikispaces page that shows the spreadsheet embedded and has links that allow students to go to the sheet and edit and enter the time they want
- push the sheet out to students with instructions (wait til Canvas has all the students)
By Saturday of 1st week - assign each student to a Team with a mentor (or two mentors) - Avery (DONE)
- maybe create a TEAMS page on Wikispaces or on Canvas for everyone to see their assignments.
- team meetings will start at the end of the 2nd Week
In 'Pigeon Holes' for lab notebooks (Sunday or Monday)
organize pigeon holes by moving VDS Alums to the other lab notebook stacks - Cidia, Nikkimake new name plate sheets (out of manila folders) - Cidia, Nikki
Organize binders (Student one and Mentor one) -
Mentor Folder:
- print new timesheet pay periods sheet (from UT webpage - Timesheet Pay Periods and Due Dates (see bottom of link) - Andee
- create and print new hourly sign-in sheet (don't need to do TA though) - see old one in GDocs either VDSStaff or /Mentors - Andee
Student Folder:Mentor name tags with VDS logo on them (talk to Dr. B - may have to use Dr. B's printer? Might work on lab printer in manual feed mode) - Brianna
- see hold name tags file in GDrive VDSclass login /Misc/NameBadgeLabels
-- create new folder /MentorsSpring15
Lab Beer's Law - Brianna, Alberto
Lab Precision & Accuracy - Nikki, John G., (do Sunday preferably)
- First pipetting steps with Excel graph
Lab Buffers & Solutions (modified solution)Calculate lowest concentration of a stock enzyme that is acceptable for enzyme assay lab (draft protocol in GDrive/VDSStaff/Spring15Labs) - Cidia
SMALL CULTURES
Put small cultures (8hrs ones) into fridge for expression tomorrow - ALL (except John and Avery)
- Melissa made several in the AM for you to use
MentorsSp13 (last year's mentors page)
M 3-4, T 4-5, F 2-3